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Francesco Nicassio

Senior Researcher - Tenured , Center Coordinator, Principal Investigator
Senior Researcher Tenured - Principal Investigator
Genomic Science
Francesco Nicassio
Research center
Interests
About

Francesco Nicassio is a tenured Senior Researcher at the Istituto Italiano di Tecnologia (IIT) and Director of the Center for Genomic Science (CGS) at IIT@SEMM in Milan, where he also leads the Genomic Science research line. He coordinates the RNA Technology Flagship at IIT, a cross-center program integrating RNA biology, RNA technologies, and translational research, and serves as faculty member at the European School of Molecular Medicine (SEMM).

His scientific activity focuses on the study of gene expression regulation mediated by non-coding RNAs and RNA regulatory mechanisms in cancer, with particular emphasis on microRNAs, long non-coding RNAs, and RNA modifications. His laboratory operates as a hybrid experimental–computational environment, combining genomics, single-cell multi-omics, long-read sequencing technologies, and CRISPR-based functional genomics to dissect regulatory networks underlying cancer plasticity, drug resistance, and disease progression.

After graduating in Biology at the University of Bari, he completed his PhD in Life Sciences at the European Institute of Oncology (IEO, Milan). He subsequently carried out postdoctoral and research activities at IFOM and IEO before joining IIT in 2012, where he established his independent research group. Since 2017, he has been coordinating the Center for Genomic Science, overseeing scientific strategy, infrastructure development, and personnel management, and in 2022 he was tenured as Senior Researcher.

Nicassio has made key contributions to RNA biology, including pioneering work on circulating microRNAs for cancer diagnostics and the identification of Target-Dependent miRNA Degradation (TDMD) as a physiologically relevant mechanism of post-transcriptional regulation. More recently, his group has contributed to the development and application of nanopore direct RNA sequencing and single-cell technologies to study RNA modifications, transcript isoforms, and regulatory heterogeneity in cancer and other disease contexts.

Beyond his research activity, he plays an active institutional and community-building role at national and European level. He serves as the Italian lead for the ELIXIR Focus Group on RNA epitranscriptomics and long-read sequencing, is a nominated member of the 1+Million Genomes Initiative (Working Group on Good Sequencing Practice), and is involved in major European initiatives on genomic data infrastructures and advanced RNA technologies.  He is actively involved in European training and research consortia, including Marie Skłodowska-Curie Doctoral Networks, and participates in international collaborative frameworks on long-read transcriptomics and RNA biology, including COST actions. He is also co-founder and scientific co-coordinator of the Milan RNA Salon, a joint IIT–Human Technopole initiative aimed at fostering interaction within the RNA research community.

Outside the laboratory, he maintains a strong interest in activities that reflect his approach to scientific research: curiosity, endurance, and exploration beyond established boundaries. He is passionate about travel and cultural experiences, including music, cinema, photography, and visual arts. Sport plays a central role in his life, with a long-standing engagement in endurance disciplines such as long-distance running, marathons, and triathlon, as well as dynamic practices including parkour and yoga, which he considers complementary tools to maintain balance, focus, and long-term sustainability in both scientific and personal life. 

Alongside his research activity, he is actively involved in public engagement and cancer awareness initiatives, contributing to outreach campaigns promoted by national organizations,such as Associazione Italiana Ricerca sul Cancro (AIRC), and regularly participating in media and public events to communicate the value of scientific research, prevention, and innovation in oncology to a broader audience.

Education

Title: PhD in Life Science
Institute: Open University, London (U.K.)
Location: Milan
Country: Italy
From: 2001 To: 2005

Title: Corso di Specializzazione post-laurea "POSTGEN - post-genomic technologies integration systems"
Institute: Università degli studi di Milano
Location: Milan
Country: Italy
From: 2001 To: 2002

Title: Laurea (vecchio ordin.) in Scienze Biologiche
Institute: Università degli studi di Milano
Location: Bari
Country: Italy
From: 1995 To: 2000

Experience External

Title: Scientific Advisor
Institute: Istituto Europeo di Oncologia (IEO)
Location: Milan
Country: Italy
From: 2012 To: 2014

Title: Scientist
Institute: Istituto Europeo di Oncologia (IEO)
Location: Milan
Country: Italy
From: 2011 To: 2011

Title: post-doctoral fellow
Institute: IFOM - FIRC Institute for Molecular Oncology
Location: Milan
Country: Italy
From: 2005 To: 2010

Title: PhD student
Institute: IFOM - FIRC Institute for Molecular Oncology
Location: Milan
Country: Italy
From: 2001 To: 2005

Title: Research Fellow
Institute: Istituto Europeo di Oncologia (IEO)
Location: Milan
Country: Italy
From: 2000 To: 2020

Skills

Manager Activities
- managing budget, personnel and facilities for the entire centre

Research Activities
- Coordinating research activity of the ‘noncoding genome lab
- scientific direction of CGS
- Securing funding
- Networking and scientific liaisons at national and international level

Teaching
- Teaching (sporadic activity) for PhD students enrolled at European School of Molecular Medicine (SEMM) - Milan

Top Publications
2024
Maestri S., Furlan M., Mulroney L., Tarrero L.C., Ugolini C., Pozza F.D., Leonardi T., Birney E., Nicassio F., Pelizzola M.
Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing
Briefings in Bioinformatics, vol. 25, (no. 2)
2024
Nadalin F., Marzi M.J., Pirra Piscazzi M., Fuentes-Bravo P., Procaccia S., Climent M., Bonetti P., Rubolino C., Giuliani B., Papatheodorou I., Marioni J.C., Nicassio F.
Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution
Nature Communications, vol. 15, (no. 1)
Article Journal
2022
Ugolini C., Mulroney L., Leger A., Castelli M., Criscuolo E., Williamson M.K., Davidson A.D., Almuqrin A., Giambruno R., Jain M., Frige G., Olsen H., Tzertzinis G., Schildkraut I., Wulf M.G., Correa I.R., Ettwiller L., Clementi N., Clementi M., Mancini N., Birney E., Akeson M., Nicassio F., Matthews D.A., Leonardi T.
Nanopore ReCappable sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs
Nucleic Acids Research, vol. 50, (no. 6), pp. 3475-3489
2022
Simeone I., Rubolino C., Noviello T.M.R., Farinello D., Cerulo L., Marzi M.J., Nicassio F.
Prediction and pan-cancer analysis of mammalian transcripts involved in target directed miRNA degradation
Nucleic Acids Research, vol. 50, (no. 4), pp. 2019-2035
2021
Tordonato C., Marzi M.J., Giangreco G., Freddi S., Bonetti P., Tosoni D., Di Fiore P.P., Nicassio F.
Mir-146 connects stem cell identity with metabolism and pharmacological resistance in breast cancer
Journal of Cell Biology, vol. 220, (no. 5)
All Publications
2025
Zampini M., Riva E., Lanino L., Sauta E., Dos Reis R.A., Ejarque R.M.A., Maggioni G., Termanini A., Merlotti A., Campagna A., Dall'Olio L., Kulasekararaj A., Calvi M., Di Vito C., Bonometti A., Rahal D., Croci G., Boveri E., Gianelli U., Ponzoni M., Caselli R., Albertazzi S., Todisco G., Ubezio M., Crisafulli L., Frigo A., Lugli E., Mosca E., Acha P., Ghisletti S., Nicassio F., Santoro A., Diez-Campelo M., Sole F., Ades L., Platzbecker U., Santini V., Fenaux P., Haferlach T., Sallman D., Garcia-Manero G., Mavilio D., Remondini D., Castellani G., D'Amico S., Zeidan A.M., Komrokji R., Kordasti S., Ficara F., Porta M.G.D.
Characterization and Clinical Implications of p53 Dysfunction in Patients With Myelodysplastic Syndromes
Journal of Clinical Oncology
2025
Lattanzi G., Strati F., Diaz-Basabe A., Perillo F., Amoroso C., Protti G., Giuffre M.R., Iachini L., Baeri A., Baldari L., Cassinotti E., Ghidini M., Galassi B., Lopez G., Noviello D., Porretti L., Trombetta E., Messuti E., Mazzarella L., Iezzi G., Nicassio F., Granucci F., Vecchi M., Caprioli F., Facciotti F.
Corrigendum to “iNKT cell-neutrophil crosstalk promotes colorectal cancer pathogenesis” [Mucosal Immunol. 16(3) (2023) 326–340 (Mucosal Immunology (2023) 16(3) (326–340), (S1933021923000247), (10.1016/j.mucimm.2023.03.006))
Mucosal Immunology
Erratum Journal
2025
Finocchiaro C., Giuliani B., Tria G., Mimani S., Ugolini C., Marzi M.J., Nicassio F.
Dissecting the contribution of non-coding elements to Breast Cancer plasticity
RNA Society Annual Meeting 2025
Poster Conference
2025
Zdravkov M., Mulroney L., Bisi S., Rubolino C., Cscujuela Tarrero L., Marzi M.J., Leonardi T., Nicassio F.
Nanocompore 2.0 – High-throughput detection of native RNA modifications by Nanopore sequencing
EMBO Workshop The epitranscriptome
Poster Conference
2024
Mulroney L., Coscujuela-Tarrero L., Maragno P., Rubolino C., Maestri S., Furlan M., Marzi M.J., Fitzgerald T., Leonardi T., Pelizzola M., Birney E., Nicassio F.
A comprehensive survey of RNA modifications in a human transcriptome
bioRxiv
Article Journal
Scientific Talks
2025
Nicassio F.
Applications and limitations of human small RNA biology in the clinic
2025 “InteRNAt” summer school:
School (Summer school, ...)
2025
Nicassio F.
Dissecting the epigenetic and transcriptional programs governing cancer stem cells through single-cell multi-omics and long-read transcriptomics
ABCD 2025 Meeting
Conference
2025
Nadalin F., Marzi M.J., Piscazzi M. P., Fuentes-Bravo P., Procaccia S., Climent M., Bonetti P., Rubolino C., Giuliani B., Papatheodorou I., Marioni J. C., Nicassio F.
Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution
RNA Society Annual Meeting 2025
Conference
2024
Nicassio F.
Cellular and molecular heterogeneity in human cancer
EpiNantes 2024 https://www.epinantes2024.com
Conference
2024
nicassio F.
CELLULAR AND MOLECULAR HETEROGENEITY IN HUMAN CANCER
Università degli studi di Milano
Institute
Awards and Achievements
2026
Nicassio F.
Nominated member of the 1+Million Genomes Initiative – Working Group 4 (Good Sequencing Practice)
2025
Nicassio F.
Elected member of the Executive Board of ABCD
Organized Events
2026
Nicassio F., Legnini I.
Co-founder and scientific co-coordinator of the Milan RNA Salon (IIT–Human Technopole)
2024
Nicassio F., Ciarrocchi E., Siciliano V.
ABCD 2024 RNA Biology and Systems Medicine
2024
Nicassio F., Siciliano V., Ciarocchi A.
ABCD Meeting on RNA and Systems Biology
2024
Picardi E., Nicassio F., De Leo F., Pesole G.
Computational Methods for Epitranscriptomics
2024
Nicassio F., Ciarocchi A., Siciliano V.
RNA biology and Systems Medicine ABCD Meeting